

Protein can be classified according to solubility,
shape or the presence of nonprotein groups, etc.
For example:
1.
2.
3.
Solubility, two major families are the globular and
fibrous protein. The globular proteins are compact, are
roughly spherical or ovoid in shape, and have axial
ratios of not over 3 (the ratio of their shortes to
longest dimention).
Composition. For example: glycoproteins, lipoproteins,
metaloproteins (that incorporate a metal ion such as
many enzyme do) etc.
Biologycal functions: enzymes, hormones,
neurotransmitters, toxin, contractile muscle (myosin
and actin), storage protein (casein, ovalbumin and
ferritin), transfort protein (hemoglobin), structural
proteins (collagen, elastine, and protein cell
membranes) and protective proteins.
Amino Acid and Protein
1
Globular Proteins
 Myoglobin, a monomeric protein of red muscle,
stores oxygen.
 Hemoglobin, a tetramic (22) protein of
eritrocytes, transport O2 to the tissue and return
CO2 and rptons to the lung. Despite different
primary structures, the secondary-tertiary
structure of subunits of hemoglobin (Hb S), Val
replaces the 6 Glu of Hb A. The genetic defect
has known as thalassemia result from theh
partial or total absence of one or more  or 
chains of hemoglobin.
Amino Acid and Protein
2
Amino Acids and the
Primary Stucture of Proteins
Important biological functions of proteins
1. Enzymes, the biochemical catalysts
2. Storage and transport of biochemical molecules
3. Physical cell support and shape (tubulin, actin,
collagen)
4. Mechanical movement (flagella, mitosis,
muscles)
(continued)
Prentice Hall c2002
Chapter 3
3
Globular proteins
• Usually water soluble, compact, roughly
spherical
• Hydrophobic interior, hydrophilic surface
• Globular proteins include enzymes,carrier
and regulatory proteins
Prentice Hall c2002
Chapter 3
4
Fibrous proteins
• Provide mechanical support
• Often assembled into large cables or threads
• -Keratins: major components of hair and nails
• Collagen: major component of tendons, skin,
bones and teeth
Prentice Hall c2002
Chapter 3
5
MYOGLOBIN STRUCTURE
Amino Acid and Protein
6
Amino Acid and Protein
7
Fibrous Proteins
 Collagen is the most abundant of the fibrous
proteins that constitute more than 25% of the
protein mass in the human body. These proteins
in bone, teeth, tendons, skin, and soft
connective tissue. Collagen forms a unique triple
helix. Every third amino acid residue in collagen
is a glycine residue. Collagen is also rich in
proline and hydroxyproline, yielding a repetitive
Gly-X-Y pattern in which Y generally is proline or
hydroxyproline (Gly-X-Y-Gly-X-Y-Gly-X-Y-).
Disease of collagen maturation include the
vitamin C deficiency disease scurvy and EhlersDanlos syndrome.
Amino Acid and Protein
8
Amino Acid and Protein
9
Prions-Protein
 Human prionrelated protein, PrP, a glycoprotein
encoded on the short arm of chromosome 20,
normally is monomeric and rich  helix.
Pathologic prion proteins, known as PrPc, is rich
in  sheet with many hydrophobic aminoacyl side
chains. Prion disease are protein conformation
diseases transmitted by altering the
conformation, fatal neurogenerative diseases
characterized by spongiform changes.
 For example: Creutzfeld-Jacob disease in
humans, scrapie in sheep, and bovine
spongiform encephalopathy (mad cow disease)
in cattle.
Amino Acid and Protein
10
Analysis of Biomolecules
ELECTROPHORESIS
Amino Acid and Protein
11
B. Amphoteric
properties
H
R–C–C
NH3+
O
H
OH–
OH
Cationic form
charge +1
pH IEP
H+
R–C–C
NH3+
H
O
O
OH–
–
Zwitter ion form
charge 0
pH IEP
H+
R–C–C
O
O–
NH2
Anionic form
charge -1
pH IEP
Amino acids are amphoteric molecules ; that is,
they have both basic and acidic groups
Monoamino-monocarboxylic acids exist in solution
neutral pH are predominantly dipolar ions (or
zwitter ion). In dipolar form of an amino acid, the
amino group is protonated and positively charged
(-NH3+) and the carboxyl group is dissociated and
negatively charged (-COO-)
Amino Acid and Protein
continued
12
Basic
Concepts
Fundamental to electrophoretical
separations is the fact that proteins are
electrically charges particles.
The charges are derived from amino
acids with ionogenic side groups.
H
R
C
NH2
Amino group
C=O
Acid group
OH
Amino Acid and Protein
13
ELECTROPHORESIS
 Electrophoresis is a method for analysis
(this is separation or isolation) and
characterization of biological polymers.
 Here is the use of electrophoresis for the
separation of proteins.
 The sample containing the proteins to be
separated is placed in an electric field
which forces the electrically charged
proteins to move.
Amino Acid and Protein
14
ELECTROPHORESIS

The movement of molecules
(in an electric field)
influenced by the
Size
Charge
Amino Acid and Protein
Shape
Chemical
composition
of the molecule
15
SEPARATION OF PROTEINS
 The separation is normally performed not in
free solution but in a supporting gel medium.
 The gel can either act as an ”inert” support
for the electrophoresis buffer or actively
participate in the separation by interacting
with the proteins
 In the latter case the protein-gel interaction is
the actual separation factor while the
electrical field merely makes the proteins
migrate through the gel
Amino Acid and Protein
16
Methods of Electrophoresis
 The major difference between methods is the
type of support medium, which can be either
cellulose or thin gels
1. Cellulose is used as a support medium
for low-molecular weight biochemicals
such as amino acids and carbohydrates
2. Polyacrylamide and agarose gels are
widely used as support media for larger
molecules.
Amino Acid and Protein
17
Methods of electrophoresis divided into
1. Polyacrylamide Gel Electrophoresis (PAGE)
2. Discontinuous Gel Electrophoresis
3. Sodium Dodecyl Sulfate-PAGE (SDS-PAGE)
4. Pulsed Field Gel Electrophoresis (PFGE)
5. Isoelectric Focusing of Protein (IEF)
6. Capillary Electrophoresis (CE)
7. Immunoelectrophoresis (IE)
Amino Acid and Protein
18